+Open data
-Basic information
Entry | Database: PDB / ID: 7ei2 | ||||||
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Title | Structure of human NNMT in complex with macrocyclic peptide 8 | ||||||
Components |
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Keywords | TRANSFERASE / Nicotinamide N-methyltransferase | ||||||
Function / homology | Function and homology information pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration / positive regulation of gluconeogenesis / : / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å | ||||||
Authors | Hayashi, K. / Mikamiyama, H. / Uehara, S. / Yamamoto, S. / Cary, D. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. ...Hayashi, K. / Mikamiyama, H. / Uehara, S. / Yamamoto, S. / Cary, D. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. / Kawai, T. / Ono, T. / Yamamoto, S. / Fumoto, M. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: Macrocyclic Peptides as a Novel Class of NNMT Inhibitors: A SAR Study Aimed at Inhibitory Activity in the Cell. Authors: Hayashi, K. / Uehara, S. / Yamamoto, S. / Cary, D.R. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. / Kawai, T. / Ono, T. / Yamamoto, S. / Fumoto, M. / Mikamiyama, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ei2.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ei2.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ei2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ei2_validation.pdf.gz | 440.1 KB | Display | wwPDB validaton report |
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Full document | 7ei2_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 7ei2_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7ei2_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/7ei2 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7ei2 | HTTPS FTP |
-Related structure data
Related structure data | 7eguC 7ehzC 3rodS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28891.164 Da / Num. of mol.: 1 / Mutation: E103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli (E. coli) References: UniProt: P40261, nicotinamide N-methyltransferase |
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#2: Protein/peptide | Mass: 1175.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium iodide, 0.1M Bis-Tris propane pH7.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.08→52 Å / Num. obs: 14497 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Χ2: 1.066 / Net I/σ(I): 17.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.464
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ROD Resolution: 2.08→51.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.809 / SU ML: 0.155 / SU R Cruickshank DPI: 0.2242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.06 Å2 / Biso mean: 46.734 Å2 / Biso min: 28.95 Å2
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Refinement step | Cycle: final / Resolution: 2.08→51.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.133 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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